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<title> BALSAC Version 2.15 Manual, Section 6.3.2</title>
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<h1>6.3.2.  STRUCTURE OPTION, [S]</h1>

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[S]  This option allows you to modify, shift, add, hide, or remove atoms of
     the cluster studied in a BALSAC/CLUSTER session. If BALSAC/CLUSTER is
     started from scratch in an interactive session (without a structure
     input file) this option defines the initial cluster where
 
          ====== STRUCTURE OPTIONS ==============
 
          Build structure from scratch
          Title (A60) :
 
     asks for a title (up to 60 ASCII characters) describing the cluster
     and
 
          No. of atoms N (&gt;0, 0=esc) :
 
     asks for the total number nct of atoms to define the cluster. (Dummy
     input nct = 0  returns to the BALSAC/CLUSTER startup menu.) This is
     followed by nt prompts
 
          1   (X,Y,Z,R,NUC) :
         ...
         nct  (X,Y,Z,R,NUC) :
 
     requesting five numbers each defining the cluster atoms by their
     positions (x,y,z) in absolute cartesian coordinates, atom radii rad and
     nuclear charges nuc. Atomic radii do not need to be known at this point
     and can be determined later, see option [R] below and Sec. <a href="./balm.87.html">6.3.3</a>. The
     initial cluster definition is confirmed by
 
            nct (nel)  different atoms (elements)
 
     where nel gives the number of elements (= atoms of different nuclear
     charge) after which BALSAC moves to the structure option menu. This
     startup input is not required if the structure option is chosen from the
     main option menu of BALSAC/CLUSTER.
 
 
     Selecting [S] from the main option menu of BALSAC/CLUSTER shows the
     structure option menu, submenu S
 
       ====== STRUCTURE OPTIONS =============================================
 
        [T]it    [R]ad/nuc  [A]toms  [G]rp  [F]ilrd  [L]ist  [S]ymm  [D]ispla
        [X]plot  [?,]esc
       ================================================================  9 ==
 
     from which atoms of the cluster can be (re)defined, listed, or plotted
     in many different ways.
 
 &gt;   [T]  selected from submenu S shows the present title of the cluster by
 
              Title [ ... old title ... ]
              New (A60,"-"=esc) :
 
          asking for a new title (up to 60 characters, longer text will be
          truncated). Answering the prompt by a one character title "-" will
          leave the present title unchanged. After title (or dummy) input
          BALSAC returns to the structure option menu S.
 
 &gt;   [R]  selected from submenu S moves to the radii/charge option menu
          allowing you to modify radii and nuclear charges of all atoms of
          the cluster. The options of this menu are explained in detail in
          Sec. <a href="./balm.87.html">6.3.3</a>. If the radii/charge option menu is closed by selecting
          [,] BALSAC returns to the structure option menu S.
 
 &gt;   [A]  selected from submenu S allows you to add, hide, move, or delete
          cluster atoms. This option can be used to rebuild parts of the
          cluster. Details of the atom modify menu are described in
          Sec. <a href="./balm.84.html">6.3.2.1</a>.
 
 &gt;   [G]  selected from submenu S allows you to define and modify groups of
          atoms of the cluster by changing their coordinates in simple
          geometric operations, store groups on external files for later use,
          and more. Details of the group modify menu are described in
          Sec. <a href="./balm.85.html">6.3.2.2</a>.
 
 &gt;   [F]  selected from submenu S allows you to include additional atoms from
          an external (PLOT3D format) file in the present cluster. Examples
          are combinations of molecules and/or lattice sections built in
          separate BALSAC sessions and joined to form a compound system. The
          prompt
 
               File name for add ("-"=esc) :
 
          asks for the name (up to 72 characters) of a (PLOT3D format) file
          defining any cluster. Dummy input "-" will immediately return to
          submenu S while a valid file name fname containing a cluster of
          nn atoms shows submenu SF
 
               nn Atoms to add:  [A]ddall  [P]rompt  [?,]esc
 
          asking for the include mode.
 
 &gt;    &gt;   [A]  selected from submenu SF includes all cluster atoms of the
               external file in the present cluster (if possible) which is
               confirmed by
 
                    nac ( nn ) atoms added from file
                    name = [ fname ]
 
               giving the number nac of new atoms included and the number nn
               of atoms stored in the external file fname. The value nac
               will be smaller than nn if the total number of atoms after the
               include process exceeds the internal maximum namax ( = 2001
               (DOS) or = 8000 (Unix)). After all atoms are included BALSAC
               returns to the structure option menu S, see Sec. <a href="./balm.83.html">6.3.2</a>.
 
 &gt;    &gt;   [P]  selected from submenu SF allows you to include selected
               cluster atoms from the external file in the present cluster.
               Here for each atom stored in the file a line
 
                    Xyz,R,Id=   x   y   z   rad   nuc   : [A]cc [I]gn [?,]esc
 
               shows the atom position (x,y,z), its radius rad and nuclear
               charge nuc. This atom can then be included in the present
               cluster by selecting [A] which is confirmed by
 
                    Atom accepted as no. ni
 
               where ni denotes the last atom of the present cluster list.
               Alternatively, the atom can be ignored by selecting [I] which
               is confirmed by
 
                    Atom ignored
 
               After the atom has been accepted/ignored the next atom of the
               file is shown. After all atoms of the external file have been
               prompted or [,] was selected in the atom prompt the message
 
                    nac ( nn ) atoms added from file
                    name = [ fname ]
 
               gives the number nac of new atoms included in the cluster and
               the total number nn of atoms stored in the external file
               fname after which BALSAC returns to the structure option
               menu S, see Sec. <a href="./balm.83.html">6.3.2</a>.
 
 &gt;    &gt;   [,]  selected from submenu SF returns to the structure option menu
               S, see Sec. <a href="./balm.83.html">6.3.2</a>, without atoms included in the present
               cluster.
 
          Note that all new atoms included from an external file will be
          automatically considered a new group of atoms overriding the former
          group definition (if it exists). Therefore, the complete set of new
          atoms may be subject to group operations such as translation or
          copying, see Sec. <a href="./balm.85.html">6.3.2.2</a>. This becomes particularly important if
          new atoms coincide with or come very close to existing atoms and
          need to be "moved out of the way" (shift the whole group by a large
          vector, group translate option).
 
 &gt;   [L]  selected from submenu S allows you to list all or selected atoms of
          a cluster. The line
 
               nct ( nel) different atoms (elements) ,  List (NA,NE) :
 
          shows the total number nct (nel) of atoms (different elements) of
          the cluster and prompts for a range of atoms [na,ne] (given as two
          integers) to be listed. For 0 &lt; na &lt;= ne &lt;= nct the positions and
          attributes of atoms no. na to ne are listed in the form
 
                Atom      X       Y       Z        R     El/Nuc     Vis
               ----------------------------------------------------------
                 na)      x       y       z        r       nuc     visbl
               na+1)      x       y       z        r       nuc     visbl
                     ...
                 ne)      x       y       z        r       nuc     visbl
 
             ** Press [C], L-click to continue;  [,], R-click to escape **
 
          where (x,y,z) are coordinates of atom no. i (i=na...ne), r its
          radius, nuc its nuclear charges, and visbl its visibility flag ("T"
          for visible or "F" for invisible, see Sec. <a href="./balm.84.html">6.3.2.1</a>). After this
          BALSAC returns to the structure option menu S. Some lines of the
          above listing may read
 
                 i )      x     y     z      r     nuc    visbl  =&gt; ieq
 
          which indicates that atoms i and ieq coincide. Coinciding atoms
          should be removed from the cluster, see options [H], [P] of the
          atom modify menu, Sec. <a href="./balm.84.html">6.3.2.1</a>.
 
 
 &gt;   [S]  selected from submenu S allows you to impose point symmetries on
          the cluster where the cluster will be completed by adding atoms (if
          needed) to achieve the required symmetry. Details of the cluster
          symmetry menu are described in Sec. <a href="./balm.86.html">6.3.2.3</a>.
 
 &gt;   [D]  selected from submenu S shows up to 10 lines of the most recent
          output generated by the graphic analysis option, see Sec. <a href="./balm.100.html">6.3.12.2</a>,
          by
 
               ============ Latest Graphics Output ==================
 
                1: Xyz,R,Id( n1)=    x    y    z    rad     nuc
                   ...
               ======================================================
 
          This allows you to look up and use numerical output from the
          analysis for input within submenu S.
 
 &gt;   [X]  selected from submenu S plots the cluster (switching to graphics
          mode (DOS) or opening a graphics window (Unix)) or lists its atom
          coordinates depending on the plot/list mode defined in the graphics
          option, see Sec. <a href="./balm.64.html">6.2.7</a>.
 
 &gt;   [,]  selected from submenu S moves to the view option menu, see
          Sec. <a href="./balm.88.html">6.3.4</a>, if the cluster is built from scratch or returns to the
          BALSAC/CLUSTER main option menu, see Sec. <a href="./balm.81.html">6.3.0</a>.
 
 
 
 

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